Computer simulations of interactions between liquid crystal molecules and polymer surfaces II. Alignment of smectic C-forming mesogens

Computer simulations have been performed to examine the behaviour of the liquid crystalline molecule 4-n-heptyl-2-fluoro-phenyl 4-n-octyloxybiphenyl-4-carboxylate (MBF) when in contact with crystalline polymer surfaces. The simulations form part of a study of the alignment interactions that are found in liquid crystal displays. MBF forms several smectic phases including a chiral smectic C* phase when suitably doped. In this paper we examine the way that layers of MBF molecules interact with the structure of the crystalline polymer surface, with the aim of understanding how molecular level interactions give rise to macroscopic phenomena such as the cone angle in ferroelectric liquid crystal devices. Molecular dynamics simulations consisting of a fixed crystalline polymer surface in contact with either a single MBF molecule or up to two layers of them (48 molecules) have been performed. A variety of simple polymer surfaces have been examined and the simulations show that the cone angle is highly dependent on the geometry of both the liquid crystal molecule and the polymer substrate. For molecules of MBF on polyethylene substrates, a cone angle of 20 is predicted, in line with experimental findings.     

Orientational and translational correlations of liquid methane over the nanometer-picosecond scales by molecular dynamics simulation and inelastic neutron scattering

Five models for the site-site intermolecular pair interactions of methane are compared in some detail and used to investigate both structural and dynamical properties of the dense liquid deuteromethane by means of molecular dynamics (MD) simulations. The orientational distribution probabilities of molecular pairs are carefully analyzed for each anisotropic potential model. We propose a revision of existing classification methods used to group the innumerable relative orientations of methane-methane pairs into six basic geometries. With this new approach, our results for the probability of the six basic categories as a function of the intermolecular distance are different from the ones present in the literature, where the role of the angular spread on the anisotropic interaction energy is not taken in full consideration and certain configurations with no significant change in the pair-potential are assigned to different categories. The analysis of the static orientational correlations in liquid methane and the prevalence of certain configurations in different ranges guide the subsequent discussion of the MD model-dependent results for the dynamic structure factor. Comparison with our inelastic neutron scattering results for liquid CD(4) at the nanometer and picosecond space and time scales allows us to confirm the full adequacy of the Tsuzuki, Uchimaru and Tanabe model of 1998 with respect to more recent potentials.     

Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.     

Water simulation model with explicit three-molecule interactions

Much effort has been directed at developing models for the computer simulation of liquid water. The simplest models involve effective two-molecule interactions, parametrized from experiment, for use in classical molecular dynamics simulations. These models have been very successful in describing the structure and dynamics of liquid water at room temperature and one atmosphere pressure. A completely successful model, however, should be robust enough to describe the properties of liquid water at other thermodynamic points, water's complicated phase diagram, heterogeneous situations like the liquid/vapor interface, ionic, and other aqueous solutions, and confined and biological water. In this paper, we develop a new classical simulation model with explicit three-molecule interactions. These interactions presumably make the model more robust in the senses described above, and since they are short-ranged, the model is efficient to simulate. The model is formulated as a perturbation from a classical two-molecule interaction model, where the forms of the correction to the two-molecule term and the three-molecule terms result from electronic structure calculations on dimers and trimers. The magnitudes of these perturbations, however, are determined empirically. The resulting model improves upon the well-known two-molecule interaction models for both static and dynamic properties.     

Comparative study of microstructural evolution during melting and crystallization

Molecular dynamics simulations, with the interaction between atoms described by a modified analytic embedded atom method, have been performed to obtain the atomic-scale details of isothermal melting in nanocrystalline Ag and crystallization from supercooled liquid. The radial distribution function and common neighbor analysis provide a visible scenario of structural evolution in the process of phase transition. The results indicate that melting at a fixed temperature in nanocrystalline materials is a continuous process, which originates from the grain boundary network. With the melting developing, the characteristic bond pairs (555), (433), and (544), existing in liquid or liquidlike phase, increase approximately linearly till completely melted. The crystallization from supercooled liquid is characterized by three characteristic stages: nucleation, rapid growth of nucleus, and slow structural relaxation. The homogeneous nucleation occurs at a larger supercooling temperature, which has an important effect on the process of crystallization and the subsequent crystalline texture. The kinetics of transition from liquid to solid is well described by the Johnson-Mehl-Avrami equation.     

Phase diagram of water between hydrophobic surfaces

Molecular dynamics simulations demonstrate that there are at least two classes of quasi-two-dimensional solid water into which liquid water confined between hydrophobic surfaces freezes spontaneously and whose hydrogen-bond networks are as fully connected as those of bulk ice. One of them is the monolayer ice and the other is the bilayer solid which takes either a crystalline or an amorphous form. Here we present the phase transformations among liquid, bilayer amorphous (or crystalline) ice, and monolayer ice phases at various thermodynamic conditions, then determine curves of melting, freezing, and solid-solid structural change on the isostress planes where temperature and intersurface distance are variable, and finally we propose a phase diagram of the confined water in the temperature-pressure-distance space.     

First-principles study of liquid gallium at ambient and high pressure

The static and dynamic properties of liquid Ga close to the melting line have been studied by first-principles molecular dynamics simulations at ambient and elevated pressure up to 5.8 GPa. Below 2.5 GPa, the nearest neighbor Ga-Ga separation shows little change, while the second and third coordination shells are compressed to shorter distances. This behavior is attributed to the gradual occupation of the interstitial sites. Detail analysis of the local geometry and dynamical behavior refutes the proposed existence of Ga(2) dimers in the liquid state. In fact, both the structure and electronic properties of the liquid are found to closely resemble that of the underlying Ga-II and Ga-III crystalline phases.     

Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.     

Atomistic simulation of structure and dynamics of columnar phases of hexabenzocoronene derivatives

Using atomistic molecular dynamics simulations we study solid and liquid crystalline columnar discotic phases formed by alkyl-substituted hexabenzocoronene mesogens. Correlations between the molecular structure, packing, and dynamical properties of these materials are established.     

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.     

A plastic phase of water from computer simulation

We report a member of ices called plastic or rotator phase, in which individual water molecules make facile rotations as in liquid state but are held tightly in an ordered structure. Molecular dynamics simulations of three classical models of water show that a plastic ice phase appears at a temperature when ice VII is heated or liquid water is cooled at high pressures above several gigapascals. A large amount of latent heat is absorbed when ice VII is transformed to the rotator phase at 590 K and 10 GPa, which is a typical characteristic of the plastic transitions for nearly spherical molecules. In addition to the spontaneous formation of plastic phase in the simulations, its existence is supported by robustness of plastic phase for hypothetical water with varying degrees of Coulombic interactions.     

The Wolf method applied to the liquid-vapor interface of water

The Wolf method for the calculation of electrostatic interactions is applied in a liquid phase and at the liquid-vapor interface of water and its results are compared with those from the Ewald sums method. Molecular dynamics simulations are performed to calculate the radial distribution functions at room temperature. The interface simulations are used to obtain the coexisting densities and surface tension along the coexistence curve. The water model is a flexible version of the extended simple point charge model. The Wolf method gives good structural results, fair coexistence densities, and poor surface tensions as compared with those obtained using the Ewald sums method.     

Molecular dynamics studies of the kinetics of phase changes in clusters III: structures, properties, and crystal nucleation of iron nanoparticle Fe331

Molecular dynamics (MD) computer simulations have been carried out to study the structures, properties, and crystal nucleation of iron nanoparticles with 331 Fe atoms or with diameter around 2 nm. Structure information for the nanoparticles was analyzed from the MD simulations. Three crystalline phases and one amorphous phase were obtained by cooling the nanoparticles from their molten droplets at different cooling rates or with different lengths of cooling time periods. Molten droplets froze into three different solid phases and a solid-solid transition from a disordered body-centered cubic (BCC) phase to an ordered BCC phase were observed during the slow cooling and the quenching processes. Properties of nanoparticle Fe₃₃₁, such as melting point, freezing temperature, heat capacity, heat of fusion, heat of crystallization, molar volume, thermal expansion coefficient, and diffusion coefficient, have been estimated. Nucleation rates of crystallization to two solid phases for Fe₃₃₁ at temperatures of 750, 800, and 850 K are presented. Both classical nucleation theory and diffuse interface theory are used to interpret our observed nucleation results. The interfacial free energy and the diffuse interface thickness between the liquid phase and two different solid phases are estimated from these nucleation theories.     

Modelling a nematic liquid crystal

The bulk phase liquid crystalline behaviour of a cyclic siloxane with a pentamethylcyclosiloxane core and biphenyl-4-allyloxybenzoate mesogens (BCS) was studied using molecular dynamics (MD) and wide angle X-ray analysis. This material exhibits partial crystallinity at room temperature and liquid crystalline behaviour above 120° C. For the MD simulations an ensemble of 27 molecules with 135 mesogenic units was simulated and a molecular mechanics force field was used to model the structural anisotropy of the siloxane molecules. Simulations were carried out both at room temperature and at an elevated temperature (425 K). Room temperature simulations showed that, contrary to our initial assumptions, the low energy molecular conformations were not cylindrical but splayed in shape. During the simulation a smectic-like, tilted layer structure was found to evolve for the cluster when full atom potentials were used, while no such development was observed when electrostatic interactions were neglected. The presence of a tilted layered structure was also suggested by the X-ray data. These results indicate that long range electrostatic interactions are significant for the molecular system under study. In order to calculate the orientational order parameter, the orientation of the molecular axis had to be determined. This was achieved by describing the mesogen shapes to be ellipsoidal and defining the principal axis of the ellipsoids to be the molecular directors. By sampling over 200 ps of simulation at 425 K, the time averaged order parameter (S) was calculated. The calculated S of 0.36 was comparable to the value of 0.4-0.45 found from the experimental data. Apart from providing insight into the relative importance of the various competing forces in the formation of the liquid crystalline phase, these simulations are also expected to be useful in predicting the mesophase behaviour of liquid crystalline systems.     

Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail

To study the effect of the alkyl tail and the terminal dipole on the stability of the liquid crystalline phase of mesogens, we have carried out molecular dynamics simulations for 1CB(4-methyl-4'-cyanobiphenyl) and 5CB(4-n-pentyl-4'-cyanobiphenyl) by using a coarse-grained model. In the coarse-grained model, a 5CB molecule is divided into the rigid part of 1CB moiety, which is represented by an ellipsoid, and the remaining flexible part which is represented by a chain of united atoms. The nonbonded potential between coarse-grained segments is represented by the generalized Gay-Berne (GB) potential and the potential parameters are determined by directly comparing the GB potential with the atomistic potentials averaged over the rotation of the mesogen around its axis. In addition, a dipole moment is placed at one end of the ellipsoid opposite to the flexible tail. The ordered state obtained in the polar 5CB model was assigned as the nematic phase, and the experimental static and dynamical properties were reproduced well by using this coarse-grained model. Both the dipole-dipole interactions and the thermal fluctuation of the flexible tail increase the positional disorder in the director direction, and stabilize the nematic phase. Thus, the nematic phase in the polar 5CB is induced by a cooperative effect of the flexible tail and the terminal dipole. It is noted that a local bilayer structure with head-to-head association is formed in the nematic phase, as experimentally observed by x-ray diffraction measurements.     

Structural Insight into IAPP-Derived Amyloid Inhibitors and Their Mechanism of Action

Designed peptides derived from the islet amyloid polypeptide (IAPP) cross-amyloid interaction surface with Aβ (termed interaction surface mimics or ISMs) have been shown to be highly potent inhibitors of Aβ amyloid self-assembly. However, the molecular mechanism of their function is not well understood. Using solution-state and solid-state NMR spectroscopy in combination with ensemble-averaged dynamics simulations and other biophysical methods including TEM, fluorescence spectroscopy and microscopy, and DLS, we characterize ISM structural preferences and interactions. We find that the ISM peptide R3-GI is highly dynamic, can adopt a β-like structure, and oligomerizes into colloid-like assemblies in a process that is reminiscent of liquid–liquid phase separation (LLPS). Our results suggest that such assemblies yield multivalent surfaces for interactions with Aβ40. Sequestration of substrates into these colloid-like structures provides a mechanistic basis for ISM function and the design of novel potent anti-amyloid molecules.     

Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution

Molecular interactions in solution are controlled by the bulk medium and by the forces originating in the structured region of the solvent close to the solutes. In this paper, a model of electrostatic and liquid-structure forces for dynamics simulations of biomolecules is presented. The model introduces information on the microscopic nature of the liquid in the vicinity of polar and charged groups and the associated non-pairwise character of the forces, thus improving upon conventional continuum representations. The solvent is treated as a polar and polarizable medium, with dielectric properties described by an inhomogeneous version of the Onsager theory. This treatment leads to an effective position-dependent dielectric permittivity that incorporates saturation effects of the electric field and the spatial variation of the liquid density. The non-pairwise additivity of the liquid-structure forces is represented by centers of force located at specific points in the liquid phase. These out-of-the-solute centers are positioned at the peaks of liquid density and exert local, external forces on the atoms of the solute. The density is calculated from a barometric law, using a Lennard-Jones-type solute-liquid effective interaction potential. The conceptual aspects of the model and its exact numerical solutions are discussed for single alkali and halide ions and for ion-pair interactions. The practical aspects of the model and the simplifications introduced for efficient computation of forces in molecular solutes are discussed in the context of polar and charged amino acid dimers. The model reproduces the contact and solvent-separated minima and the desolvation barriers of intermolecular potentials of mean force of amino acid dimers, as observed in atomistic dynamics simulations. Possible refinements based on an improved treatment of molecular correlations are discussed.     

Structural and dynamical properties of solid ammonia borane under high pressure

The structural and dynamical properties of solid ammonia borane were investigated by means of extensive density functional theory calculation up to 60 GPa. Molecular dynamics simulations suggest that the Cmc2(1) phase found by recent room-temperature x-ray diffraction experiments can be obtained from the Pmn2(1) structure at high pressure and low temperature. Two new high-pressure phases were found on further compression at room temperature. We also found that all three high-pressure phases have proton-ordered structures, and the separation of the NH(3) and BH(3) rotation observed in the simulations can be explained by their distinct rotational energy barriers. The role of dihydrogen bonds in the high-pressure phases is discussed.